Allen was admitted to the
bar in 1825 and commenced practice in
Brattleboro, Vermont. In 1828 he married Sarah Elizabeth Fessenden. They had four children, but she died in 1845.[2] In 1830 he moved to
Bangor, Maine and entered into practice with John Appleton (born 1804), who would subsequently become Chief Justice of the Maine Supreme Court. Appleton would also marry Allen's sister Sarah in 1834.[3] Allen was a member of Bangor's first City Council, from 1834, and from 1835 to 1840 was a member of the
Maine House of Representatives, representing Bangor. He served as its Speaker in 1838. From 1841 until 1843, he served in the
U.S. House of Representatives as a member of the
Whig party, but his district (
Maine's 8th congressional district) was eliminated before the next election based on census data. He ran in the 1842 election against
Hannibal Hamlin but was defeated.[4]

In June 1856 he sailed back to
New England and married Mary Harrod Hobbs (sometimes spelled Hobbes) in Philadelphia on March 11, 1857.[7] Mary was daughter of another former Maine legislator Frederick Hobbs.
The couple returned to Honolulu, where from June 1857 through February 1877 Allen was Chief Justice of the Kingdom of Hawaii Supreme Court.[6]
During Kamehameha IV and
Queen Emma's wedding in 1856, he offered his own wedding band to the king to allow the ceremony to continue. The Allens' first-born son Frederick Hobbs (Hobbes) Allen was born ten days after
Prince Albert Edward Kauikeaouli Kaleiopapa, and the two children became playmates.[7] The prince died when he was only four years old. Frederick would serve as his father's secretary, graduate from
Harvard Law School in 1883, and become a law partner of his firm Adams & Allen in New York.[2]

He returned briefly to Hawaii, but his two children from his second marriage were back in the United States, so he resigned his supreme court post and went back to Washington in February 1877. The plantation did not live up to his hopes. By 1879 it was losing money, in debt with a mortgage, and needed a new manager. He wondered if it was doomed to a fate similar to the prince for which it was named. Finally the plantation paid dividents starting in 1882. Shortly before his seventy-ninth birthday, he died while attending a New Year's Day diplomatic reception January 1, 1883 given by President
Chester Arthur at the
White House.[5] He is interred in
Mount Auburn Cemetery in
Cambridge, Massachusetts. Allen is one of ten people known to have died inside the White House.[8]